Fst matrix 2017 samples
## TB17 PWS17 SS17 BC17 WA17 CA17
## TB17 0.00 0.33 0.30 0.39 0.30 0.41
## PWS17 0.33 0.00 0.05 0.06 0.18 0.12
## SS17 0.30 0.05 0.00 0.14 0.12 0.20
## BC17 0.39 0.06 0.14 0.00 0.26 0.05
## WA17 0.30 0.18 0.12 0.26 0.00 0.29
## CA17 0.41 0.12 0.20 0.05 0.29 0.00
Note: Very low divergence between CA and BC. Also, much higher divergence between CA and WA than CA and PWS.
Fst matrix temporal samples (within population comparisons)
## PWS91 PWS96 PWS07 PWS17
## PWS91 0.00 0.04 0.21 0.07
## PWS96 0.04 0.00 0.17 0.01
## PWS07 0.21 0.17 0.00 0.13
## PWS17 0.07 0.01 0.13 0.00
## TB91 TB96 TB06 TB17
## TB91 0.00 0.24 0.01 0.24
## TB96 0.24 0.00 0.27 0.03
## TB06 0.01 0.27 0.00 0.27
## TB17 0.24 0.03 0.27 0.00
## SS96 SS06 SS17
## SS96 0.00 0.02 0.07
## SS06 0.02 0.00 0.07
## SS17 0.07 0.07 0.00
Note: High Fst between PWS91 and PWS07. Also, high Fst between TB91 and TB96 despite low Fst between TB91 and TB06.
Fst and PBS by chromosome (3 population comparison)
Note: Very low divergence between BC and CA (as seen in matrix), but very sharp peaks of divergence on chrs 7, 12, 20, 25.
Fst and PBS by chromosome (3 population comparison)
Note: Same peaks of divergence between CA and PWS/SS on chrs 7, 12, 20.
Fst and PBS by chromosome (3 population comparison)
Note: Consistent peaks on chr 6 (also true when including PWS17).
Fst and PBS by chromosome (3 population comparison)
Fst and PBS by chromosome (3 population comparison)
Fst outliers and GO enrichment for Chr 6
## [1] " genes (Danio orthologs) within 50kb Fst outlier window (genome-wide mean > 99%ile)"
## [1] "rpp25b" "gpm6aa" "spata4" "asb5a" "ppid"
## [6] "htr4" "elp4" "pax6b" "rcn1" "mctp2b"
## [11] "MEF2A" "lrrc28" "tent4b" "sall1a" "irx6a"
## [16] "mmp2" "lpcat2" "slc6a2" "dpep2" "nfatc3a"
## [21] "galr1b" "zgc:112160" "zgc:136461" "agrp" "atp6v0d1"
## [26] "hsd11b2" "tppp3" "plekhg4" "slc9a5" "fhod1"
## [31] "rfx7a" "cln6a" "hipk3b" "spon1a" "syt9a"
## [36] "ppfibp2a" "MAF" "CDYL2" "cenpn" "atmin"
## [41] "myo9aa" "gramd2aa" "znf609b" "trip4" "drd4b"
## [46] "KIAA0895L" "GABARAPL2" "kcng4b" "ist1" "dhodh"
## [51] "prmt3" "slc6a5" "NELL1" "luzp2"
GO enrichment for 54 genes
Fst outliers and GO enrichment for CA v PWS chr 7
## [1] "66 genes (Danio orthologs) within 50kb Fst outlier window (genome-wide mean > 99%ile)"
## [1] "si:ch73-138n13.1" "kazald3" "crybb2"
## [4] "dok2" "gfra2a" "lzts1"
## [7] "cox6a1" "hps4" "hnf1a"
## [10] "zgc:162025" "lrrc75ba" "ggt5a"
## [13] "asphd2" "cabp1a" "mlec"
## [16] "pop5" "olfml2a" "arpc5la"
## [19] "golga1" "si:ch211-158d24.2" "ddx31"
## [22] "ak8" "spaca9" "grin1b"
## [25] "ptgesl" "odf2b" "gle1"
## [28] "zgc:136963" "ctu1" "pxnb"
## [31] "citb" "cux2b" "pptc7b"
## [34] "med27" "NTNG2" "slc23a2"
## [37] "ccdc92" "ciao1" "snrnp200"
## [40] "slc20a1a" "vgll4l" "syn1"
## [43] "gapvd1" "lmx1bb" "zbtb34"
## [46] "ralgps1" "angptl2b" "RNF122"
## [49] "inpp5l" "nkx6.3" "tmem127"
## [52] "es1" "igsf9b" "bnip3la"
## [55] "LRRTM4" "lrrtm4l2" "vsig8b"
## [58] "dock5" "specc1la" "adora2aa"
## [61] "upb1" "gucd1" "snrpd3"
## [64] "p2rx4b" "p2rx7"
GO enrichment for 66 genes
